Currently, there isn't an option to create a change order with a negative balance.
On an estimate, you can only put a negative amount if the total balance of the transaction will not be negative. For example, you have multiple items on the estimate that had a total amount of $50 and each item had an amount of $10. You can enter a negative amount of one or two items unless the total amount of the transaction will not be negative. I've attached a screenshot below for your reference.
So for a single transaction, you can't enter a negative amount on an estimate since this meant for an income. I want to let you know that we're taking note of your feedback and suggestions to improve the experience we're providing.
The solution would be to switch to QuickBooks Contractor Edition. While it does not allow you to record a negative change order, it does allow you revise the estimate and records the original and changes made to that estimate.
You only other alternative is add a subtotal line to your original estimate then enter the change order as a negative and subtotal again so that you have the original estimate and a record of the changes.